Propionic acid (PA) is widely used in the food industry as a food preservative. PA has also found use as a precursor for the synthesis of polymers, including but not limited to polypropylene and vinyl propionate. In addition propanol and other valuable chemicals can be derived from PA. PA has traditionally been derived from fossil fuels until recently when mounting environmental concerns have shifted end users' interest to a sustainable alternative. This search for sustainable alternatives has revived bacterial fermentation as an alternative for the production of C3 chemicals.
Propionibacterium sp are pleomorphic rods, gram-positive bacteria that naturally produce PA as their main fermentation product through the Wood-Werckman cycle. Natively, PA is produced along with other organic acids (lactate, succinate, and acetate) resulting in low productivities and modest yields which translate in costly downstream processes. Until recently, metabolic engineering in P. acidipropionici had proven to be challenging mainly due to the seven Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) which provide resistance against conjugative plasmids and bacteriophages. As disclosed herein genome shuffling (GS) can be used to improve the growth rate and PA production of P. acidipropionici. 
Originally described in the mid 70's as protoplast fusion, GS has been extensively used in industry. Examples include increased production of tylosin in Streptomyces fradiae (Zhang et al., Nature, 2002, 415, 644-646), ethanol in Saccharomyces cerevisiae (L. Hou, Appl. Biochem. Biotechnol., 2010, 160, 1084-1093), vitamin B12 in P. shermanii (Zhang et al., J. Biotechnol., 2010, 148, 139-143), lactic acid in Lactobacillus (Patnaik et al., Nat. Biotechnol., 2002, 20, 707-12), 1,3-propanediol in Clostridium diolis (Otte et al., Appl. Environ. Microbiol., 2009, 75, 7610-7616), and PA in P. acidipropionici (Guan et al., “Genome-Shuffling Improves Acid Tolerance . . . ” in Advances in Chemistry Research, Vol 15, Chapter 8 (2012) Nova Science Publishers, Inc., pp 143-152) amongst others.
To obtain Propionibacterium strains with higher propionic acid yields and lower byproducts, a genome shuffling (GS) protocol has been used to transfer genetic material between two strains of Propionibacterium resulting in novel strains with the potential for improved propionic acid production. GS combines the advantages of multi-parental crossing facilitated by DNA exchange, where the donor provides a small amount of DNA material leaving the rest of the recipient intact. The end result of GS is genetically unique strains with potentially novel pathways and regulatory mechanisms.
Previous attempts to use GS for enhancing PA production have not delivered strains with the desired phenotypes. This is due in part to the lack of genomic diversity in the known strains used in such procedures. Thus, previous efforts have failed to produce Propionibacterium strains that are capable of producing propionic acid in excess of 0.54 g/g using glucose or sucrose fermentations, that also retain multiple byproducts in appreciable quantities (Stowers et al., J. Ind. Microbiol. Biotechnol., 2014, 41, 837-852).
Accordingly, the success of using GS for enhancing PA production is predicated on the ability to select two strains with desirable phenotypes that if combined could result in an advantaged propionic acid production strain. Applicants have selected strains of Propionibacterium that they have identified as having high potential for propionic acid production. These selected strains have now been used to produce novel strains of Propionibacterium that have improved growth rates, enhanced propionic acid production (e.g., exceeding 0.54 g/g) and optionally, a reduced production of undesired byproducts such as acetic acid and succinic acid.